Starting phenix.real_space_refine on Mon Sep 14 03:20:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vmd_21240/09_2026/6vmd_21240.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vmd_21240/09_2026/6vmd_21240.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vmd_21240/09_2026/6vmd_21240.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vmd_21240/09_2026/6vmd_21240.map" model { file = "/net/cci-nas-00/data/ceres_data/6vmd_21240/09_2026/6vmd_21240.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vmd_21240/09_2026/6vmd_21240.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6vmd_21240/09_2026/6vmd_21240.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vmd_21240/09_2026/6vmd_21240.cif" } resolution = 4.53 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 14 5.49 5 S 106 5.16 5 C 17268 2.51 5 N 4746 2.21 5 O 5367 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 138 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27501 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3850 Classifications: {'peptide': 501} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 483} Chain: "B" Number of atoms: 3862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3862 Classifications: {'peptide': 503} Link IDs: {'PTRANS': 17, 'TRANS': 485} Chain: "C" Number of atoms: 3843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3843 Classifications: {'peptide': 500} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 482} Chain: "D" Number of atoms: 3619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3619 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 452} Chain: "E" Number of atoms: 3645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3645 Classifications: {'peptide': 481} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 455} Chain: "F" Number of atoms: 3636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3636 Classifications: {'peptide': 480} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 454} Chain: "d" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1384 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 4, 'TRANS': 174} Chain: "e" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1007 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 126} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "g" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2504 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 310} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.63, per 1000 atoms: 0.20 Number of scatterers: 27501 At special positions: 0 Unit cell: (155.76, 148.68, 128.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 106 16.00 P 14 15.00 O 5367 8.00 N 4746 7.00 C 17268 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS g 240 " - pdb=" SG CYS g 246 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.36 Conformation dependent library (CDL) restraints added in 1.1 seconds 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6574 Finding SS restraints... Secondary structure from input PDB file: 123 helices and 28 sheets defined 46.3% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 6 through 25 removed outlier: 3.597A pdb=" N SER A 10 " --> pdb=" O ALA A 6 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ARG A 16 " --> pdb=" O ILE A 12 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N GLY A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 177 through 186 Processing helix chain 'A' and resid 187 through 191 removed outlier: 3.848A pdb=" N GLN A 190 " --> pdb=" O GLN A 187 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASN A 191 " --> pdb=" O GLN A 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 187 through 191' Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 232 through 253 Proline residue: A 240 - end of helix Processing helix chain 'A' and resid 263 through 277 Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 288 through 289 No H-bonds generated for 'chain 'A' and resid 288 through 289' Processing helix chain 'A' and resid 290 through 300 Processing helix chain 'A' and resid 323 through 326 Processing helix chain 'A' and resid 329 through 339 removed outlier: 4.000A pdb=" N THR A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN A 334 " --> pdb=" O TYR A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 353 Processing helix chain 'A' and resid 367 through 372 removed outlier: 4.060A pdb=" N ALA A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 381 removed outlier: 3.550A pdb=" N LYS A 377 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 399 removed outlier: 4.602A pdb=" N PHE A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 421 Processing helix chain 'A' and resid 430 through 443 removed outlier: 4.245A pdb=" N THR A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 468 removed outlier: 4.241A pdb=" N TYR A 457 " --> pdb=" O GLN A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 480 removed outlier: 4.192A pdb=" N GLN A 473 " --> pdb=" O LYS A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 505 Processing helix chain 'B' and resid 9 through 18 Processing helix chain 'B' and resid 101 through 105 removed outlier: 4.128A pdb=" N TYR B 104 " --> pdb=" O SER B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 177 through 187 removed outlier: 3.719A pdb=" N GLN B 187 " --> pdb=" O THR B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 216 removed outlier: 3.595A pdb=" N VAL B 206 " --> pdb=" O LYS B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 252 Proline residue: B 240 - end of helix removed outlier: 3.665A pdb=" N PHE B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 278 Processing helix chain 'B' and resid 283 through 287 removed outlier: 3.870A pdb=" N ALA B 286 " --> pdb=" O GLY B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 300 Processing helix chain 'B' and resid 329 through 339 Processing helix chain 'B' and resid 346 through 353 removed outlier: 3.531A pdb=" N PHE B 350 " --> pdb=" O SER B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 371 removed outlier: 4.252A pdb=" N ALA B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 396 removed outlier: 5.552A pdb=" N LYS B 382 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU B 392 " --> pdb=" O ALA B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 421 Processing helix chain 'B' and resid 430 through 444 removed outlier: 3.842A pdb=" N VAL B 435 " --> pdb=" O VAL B 431 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N THR B 440 " --> pdb=" O MET B 436 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N GLY B 441 " --> pdb=" O THR B 437 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR B 442 " --> pdb=" O ILE B 438 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN B 443 " --> pdb=" O TYR B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 469 removed outlier: 3.857A pdb=" N LYS B 466 " --> pdb=" O ARG B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 479 removed outlier: 4.278A pdb=" N GLN B 473 " --> pdb=" O LYS B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 503 removed outlier: 3.992A pdb=" N GLU B 496 " --> pdb=" O GLU B 492 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN B 497 " --> pdb=" O ALA B 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 20 Processing helix chain 'C' and resid 101 through 105 removed outlier: 4.117A pdb=" N TYR C 104 " --> pdb=" O SER C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 157 Processing helix chain 'C' and resid 175 through 187 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 218 through 221 Processing helix chain 'C' and resid 232 through 253 removed outlier: 3.668A pdb=" N GLN C 236 " --> pdb=" O PRO C 232 " (cutoff:3.500A) Proline residue: C 240 - end of helix Processing helix chain 'C' and resid 263 through 278 Processing helix chain 'C' and resid 283 through 287 removed outlier: 3.591A pdb=" N ALA C 286 " --> pdb=" O GLY C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 289 No H-bonds generated for 'chain 'C' and resid 288 through 289' Processing helix chain 'C' and resid 290 through 300 Processing helix chain 'C' and resid 329 through 339 Processing helix chain 'C' and resid 346 through 352 Processing helix chain 'C' and resid 373 through 393 removed outlier: 3.812A pdb=" N LYS C 378 " --> pdb=" O LYS C 374 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LYS C 382 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU C 383 " --> pdb=" O VAL C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 399 removed outlier: 3.649A pdb=" N GLN C 398 " --> pdb=" O ALA C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 421 removed outlier: 4.110A pdb=" N GLN C 410 " --> pdb=" O ALA C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 444 removed outlier: 4.100A pdb=" N MET C 436 " --> pdb=" O GLU C 432 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR C 437 " --> pdb=" O GLU C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 469 Processing helix chain 'C' and resid 469 through 480 Processing helix chain 'C' and resid 483 through 504 Processing helix chain 'D' and resid 103 through 107 removed outlier: 3.650A pdb=" N LEU D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 159 Processing helix chain 'D' and resid 177 through 190 removed outlier: 3.818A pdb=" N ILE D 182 " --> pdb=" O LYS D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 220 Processing helix chain 'D' and resid 245 through 263 removed outlier: 4.604A pdb=" N GLY D 250 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LEU D 251 " --> pdb=" O MET D 247 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE D 260 " --> pdb=" O MET D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 289 removed outlier: 3.933A pdb=" N PHE D 278 " --> pdb=" O ASN D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 311 Processing helix chain 'D' and resid 336 through 344 removed outlier: 4.012A pdb=" N THR D 342 " --> pdb=" O ALA D 338 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA D 344 " --> pdb=" O ALA D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 358 removed outlier: 3.935A pdb=" N ALA D 357 " --> pdb=" O SER D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 381 Processing helix chain 'D' and resid 381 through 408 removed outlier: 5.218A pdb=" N ASP D 403 " --> pdb=" O LYS D 399 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ILE D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 413 removed outlier: 3.504A pdb=" N GLU D 412 " --> pdb=" O GLY D 409 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU D 413 " --> pdb=" O LEU D 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 409 through 413' Processing helix chain 'D' and resid 414 through 431 Processing helix chain 'D' and resid 436 through 440 removed outlier: 3.664A pdb=" N GLU D 439 " --> pdb=" O PHE D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 463 Processing helix chain 'D' and resid 470 through 475 removed outlier: 3.774A pdb=" N PHE D 474 " --> pdb=" O GLU D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 492 Processing helix chain 'E' and resid 153 through 159 Processing helix chain 'E' and resid 177 through 192 removed outlier: 3.749A pdb=" N LEU E 181 " --> pdb=" O GLY E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 220 removed outlier: 3.642A pdb=" N GLY E 220 " --> pdb=" O MET E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 265 removed outlier: 4.156A pdb=" N ARG E 246 " --> pdb=" O PRO E 242 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG E 248 " --> pdb=" O GLY E 244 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLY E 250 " --> pdb=" O ARG E 246 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N LEU E 251 " --> pdb=" O MET E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 290 removed outlier: 3.598A pdb=" N PHE E 278 " --> pdb=" O ASN E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 311 Processing helix chain 'E' and resid 329 through 333 removed outlier: 3.769A pdb=" N ASP E 332 " --> pdb=" O VAL E 329 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP E 333 " --> pdb=" O PRO E 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 329 through 333' Processing helix chain 'E' and resid 336 through 344 Processing helix chain 'E' and resid 353 through 360 removed outlier: 4.305A pdb=" N LYS E 359 " --> pdb=" O GLY E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 381 Processing helix chain 'E' and resid 381 through 409 removed outlier: 4.892A pdb=" N ASP E 403 " --> pdb=" O LYS E 399 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ILE E 404 " --> pdb=" O GLU E 400 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA E 406 " --> pdb=" O GLN E 402 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE E 407 " --> pdb=" O ASP E 403 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU E 408 " --> pdb=" O ILE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 431 Processing helix chain 'E' and resid 451 through 463 Processing helix chain 'E' and resid 470 through 474 Processing helix chain 'E' and resid 479 through 496 removed outlier: 3.595A pdb=" N LYS E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 158 Processing helix chain 'F' and resid 179 through 193 removed outlier: 4.566A pdb=" N LYS F 191 " --> pdb=" O ASN F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 220 Processing helix chain 'F' and resid 242 through 247 Processing helix chain 'F' and resid 248 through 263 removed outlier: 3.567A pdb=" N PHE F 260 " --> pdb=" O MET F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 287 removed outlier: 3.969A pdb=" N PHE F 278 " --> pdb=" O ASN F 274 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ALA F 287 " --> pdb=" O SER F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 312 removed outlier: 3.998A pdb=" N GLU F 305 " --> pdb=" O THR F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 333 removed outlier: 3.878A pdb=" N ASP F 332 " --> pdb=" O VAL F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 346 removed outlier: 3.628A pdb=" N ALA F 344 " --> pdb=" O ALA F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 359 removed outlier: 4.037A pdb=" N ALA F 357 " --> pdb=" O SER F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 381 Processing helix chain 'F' and resid 382 through 406 removed outlier: 4.564A pdb=" N ASP F 403 " --> pdb=" O LYS F 399 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ILE F 404 " --> pdb=" O GLU F 400 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA F 406 " --> pdb=" O GLN F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 431 Processing helix chain 'F' and resid 437 through 441 removed outlier: 3.868A pdb=" N VAL F 440 " --> pdb=" O VAL F 437 " (cutoff:3.500A) Processing helix chain 'F' and resid 451 through 463 Processing helix chain 'F' and resid 479 through 496 removed outlier: 4.342A pdb=" N LYS F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Processing helix chain 'd' and resid 73 through 89 removed outlier: 3.926A pdb=" N TYR d 78 " --> pdb=" O THR d 74 " (cutoff:3.500A) Processing helix chain 'd' and resid 91 through 106 removed outlier: 3.692A pdb=" N ARG d 104 " --> pdb=" O GLU d 100 " (cutoff:3.500A) Processing helix chain 'd' and resid 109 through 117 Processing helix chain 'd' and resid 121 through 137 removed outlier: 3.662A pdb=" N GLY d 137 " --> pdb=" O ILE d 133 " (cutoff:3.500A) Processing helix chain 'd' and resid 139 through 152 removed outlier: 3.907A pdb=" N ILE d 146 " --> pdb=" O THR d 142 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASN d 147 " --> pdb=" O ALA d 143 " (cutoff:3.500A) Processing helix chain 'd' and resid 154 through 156 No H-bonds generated for 'chain 'd' and resid 154 through 156' Processing helix chain 'd' and resid 157 through 174 removed outlier: 4.488A pdb=" N GLU d 166 " --> pdb=" O LEU d 162 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ASP d 167 " --> pdb=" O ASN d 163 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL d 168 " --> pdb=" O GLU d 164 " (cutoff:3.500A) Processing helix chain 'd' and resid 187 through 202 Processing helix chain 'd' and resid 237 through 249 removed outlier: 4.027A pdb=" N GLU d 243 " --> pdb=" O LYS d 239 " (cutoff:3.500A) Processing helix chain 'e' and resid 88 through 103 Processing helix chain 'e' and resid 109 through 131 removed outlier: 3.797A pdb=" N ILE e 113 " --> pdb=" O LYS e 109 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU e 114 " --> pdb=" O ARG e 110 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU e 127 " --> pdb=" O ARG e 123 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA e 128 " --> pdb=" O THR e 124 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER e 129 " --> pdb=" O ARG e 125 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR e 131 " --> pdb=" O GLU e 127 " (cutoff:3.500A) Processing helix chain 'g' and resid 42 through 100 Proline residue: g 84 - end of helix Processing helix chain 'g' and resid 133 through 152 removed outlier: 3.685A pdb=" N LEU g 151 " --> pdb=" O GLU g 147 " (cutoff:3.500A) Processing helix chain 'g' and resid 163 through 171 removed outlier: 3.709A pdb=" N ARG g 171 " --> pdb=" O TYR g 167 " (cutoff:3.500A) Processing helix chain 'g' and resid 187 through 204 removed outlier: 3.604A pdb=" N SER g 204 " --> pdb=" O SER g 200 " (cutoff:3.500A) Processing helix chain 'g' and resid 287 through 361 removed outlier: 3.515A pdb=" N LEU g 292 " --> pdb=" O PRO g 288 " (cutoff:3.500A) Proline residue: g 297 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 55 removed outlier: 3.507A pdb=" N GLY A 30 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ARG A 41 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL A 35 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE A 39 " --> pdb=" O VAL A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 98 removed outlier: 3.548A pdb=" N ILE A 98 " --> pdb=" O ARG A 128 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG A 128 " --> pdb=" O ILE A 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 109 removed outlier: 6.018A pdb=" N ILE A 109 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE A 193 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ILE A 260 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N VAL A 195 " --> pdb=" O ILE A 260 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 319 through 321 Processing sheet with id=AA5, first strand: chain 'B' and resid 39 through 43 removed outlier: 7.550A pdb=" N ASN B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N LEU B 67 " --> pdb=" O ASN B 71 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N GLY B 73 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU B 65 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU B 52 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LEU B 53 " --> pdb=" O THR B 92 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 39 through 43 removed outlier: 7.550A pdb=" N ASN B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N LEU B 67 " --> pdb=" O ASN B 71 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N GLY B 73 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU B 65 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN D 25 " --> pdb=" O ASP D 32 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ARG D 73 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN D 67 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL D 77 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL D 65 " --> pdb=" O VAL D 77 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 147 removed outlier: 4.170A pdb=" N VAL B 160 " --> pdb=" O LEU B 147 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 168 through 170 removed outlier: 3.656A pdb=" N VAL B 320 " --> pdb=" O ILE B 168 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 222 through 223 removed outlier: 5.840A pdb=" N ILE B 193 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE B 260 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL B 195 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N LEU B 317 " --> pdb=" O THR B 257 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE B 259 " --> pdb=" O LEU B 317 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 91 through 93 removed outlier: 3.877A pdb=" N ASN E 45 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL E 65 " --> pdb=" O ASN E 45 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL E 65 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N VAL E 77 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN E 67 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ALA E 34 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ILE E 23 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ASN C 28 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ALA d 178 " --> pdb=" O LYS d 210 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL d 212 " --> pdb=" O ALA d 178 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N VAL d 180 " --> pdb=" O VAL d 212 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 91 through 93 removed outlier: 3.877A pdb=" N ASN E 45 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL E 65 " --> pdb=" O ASN E 45 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL E 65 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N VAL E 77 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN E 67 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ALA E 34 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ILE E 23 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY C 73 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N LEU C 67 " --> pdb=" O ASN C 71 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ASN C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N HIS C 43 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL C 32 " --> pdb=" O HIS C 43 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ALA d 178 " --> pdb=" O LYS d 210 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL d 212 " --> pdb=" O ALA d 178 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N VAL d 180 " --> pdb=" O VAL d 212 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 98 through 100 Processing sheet with id=AB4, first strand: chain 'C' and resid 108 through 109 removed outlier: 3.645A pdb=" N ILE C 109 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA C 226 " --> pdb=" O ILE C 109 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N VAL C 225 " --> pdb=" O CYS C 194 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N TYR C 196 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N GLU C 227 " --> pdb=" O TYR C 196 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA C 198 " --> pdb=" O GLU C 227 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE C 193 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N ILE C 260 " --> pdb=" O ILE C 193 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL C 195 " --> pdb=" O ILE C 260 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 146 through 147 removed outlier: 4.643A pdb=" N VAL C 160 " --> pdb=" O LEU C 147 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 99 through 101 Processing sheet with id=AB7, first strand: chain 'D' and resid 110 through 111 removed outlier: 7.739A pdb=" N LEU D 234 " --> pdb=" O PHE D 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 148 through 149 removed outlier: 3.586A pdb=" N PHE D 149 " --> pdb=" O TYR D 162 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N TYR D 162 " --> pdb=" O PHE D 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 197 through 199 removed outlier: 7.286A pdb=" N LEU D 270 " --> pdb=" O ILE D 324 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N ALA D 326 " --> pdb=" O LEU D 270 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N ILE D 272 " --> pdb=" O ALA D 326 " (cutoff:3.500A) removed outlier: 9.026A pdb=" N TYR D 328 " --> pdb=" O ILE D 272 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY D 172 " --> pdb=" O VAL D 327 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N PHE D 171 " --> pdb=" O LEU D 352 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 99 through 100 Processing sheet with id=AC2, first strand: chain 'E' and resid 110 through 111 removed outlier: 3.877A pdb=" N ALA E 233 " --> pdb=" O SER E 197 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL E 198 " --> pdb=" O PHE E 271 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N VAL E 268 " --> pdb=" O THR E 322 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE E 324 " --> pdb=" O VAL E 268 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU E 270 " --> pdb=" O ILE E 324 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ILE E 168 " --> pdb=" O GLN E 325 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N THR E 350 " --> pdb=" O LYS E 167 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N GLY E 169 " --> pdb=" O THR E 350 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 30 through 31 removed outlier: 3.534A pdb=" N GLN F 67 " --> pdb=" O ARG F 75 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL F 77 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N VAL F 65 " --> pdb=" O VAL F 77 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 99 through 101 Processing sheet with id=AC5, first strand: chain 'F' and resid 110 through 111 removed outlier: 6.186A pdb=" N VAL F 198 " --> pdb=" O PHE F 271 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE F 168 " --> pdb=" O GLN F 325 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 148 through 149 removed outlier: 4.307A pdb=" N TYR F 162 " --> pdb=" O PHE F 149 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'e' and resid 13 through 14 removed outlier: 6.009A pdb=" N LEU e 8 " --> pdb=" O VAL e 78 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'e' and resid 48 through 52 removed outlier: 3.525A pdb=" N ALA e 61 " --> pdb=" O GLU e 82 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'g' and resid 156 through 159 removed outlier: 3.576A pdb=" N ILE g 158 " --> pdb=" O LEU g 120 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU g 211 " --> pdb=" O ALA g 119 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS g 228 " --> pdb=" O MET g 212 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS g 216 " --> pdb=" O ASP g 224 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ASP g 224 " --> pdb=" O LYS g 216 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'g' and resid 251 through 257 1269 hydrogen bonds defined for protein. 3687 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.75 Time building geometry restraints manager: 3.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9292 1.34 - 1.46: 5561 1.46 - 1.59: 12809 1.59 - 1.71: 21 1.71 - 1.83: 200 Bond restraints: 27883 Sorted by residual: bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.29e+01 bond pdb=" C4 ATP D 601 " pdb=" C5 ATP D 601 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.28e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.12e+01 bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 4.98e+01 bond pdb=" C5 ATP C 600 " pdb=" C6 ATP C 600 " ideal model delta sigma weight residual 1.409 1.472 -0.063 1.00e-02 1.00e+04 3.94e+01 ... (remaining 27878 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.03: 37551 5.03 - 10.05: 213 10.05 - 15.08: 13 15.08 - 20.10: 4 20.10 - 25.13: 5 Bond angle restraints: 37786 Sorted by residual: angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 114.74 25.13 1.00e+00 1.00e+00 6.31e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 116.60 23.27 1.00e+00 1.00e+00 5.41e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 117.18 22.69 1.00e+00 1.00e+00 5.15e+02 angle pdb=" PA ATP B 600 " pdb=" O3A ATP B 600 " pdb=" PB ATP B 600 " ideal model delta sigma weight residual 136.83 114.63 22.20 1.00e+00 1.00e+00 4.93e+02 angle pdb=" PB ATP D 601 " pdb=" O3B ATP D 601 " pdb=" PG ATP D 601 " ideal model delta sigma weight residual 139.87 119.34 20.53 1.00e+00 1.00e+00 4.21e+02 ... (remaining 37781 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.35: 15584 22.35 - 44.70: 1256 44.70 - 67.05: 161 67.05 - 89.40: 56 89.40 - 111.74: 1 Dihedral angle restraints: 17058 sinusoidal: 6816 harmonic: 10242 Sorted by residual: dihedral pdb=" CA ALA D 295 " pdb=" C ALA D 295 " pdb=" N VAL D 296 " pdb=" CA VAL D 296 " ideal model delta harmonic sigma weight residual -180.00 -127.28 -52.72 0 5.00e+00 4.00e-02 1.11e+02 dihedral pdb=" CA ALA F 295 " pdb=" C ALA F 295 " pdb=" N VAL F 296 " pdb=" CA VAL F 296 " ideal model delta harmonic sigma weight residual -180.00 -132.27 -47.73 0 5.00e+00 4.00e-02 9.11e+01 dihedral pdb=" CA ALA E 295 " pdb=" C ALA E 295 " pdb=" N VAL E 296 " pdb=" CA VAL E 296 " ideal model delta harmonic sigma weight residual -180.00 -134.50 -45.50 0 5.00e+00 4.00e-02 8.28e+01 ... (remaining 17055 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 3708 0.080 - 0.159: 676 0.159 - 0.239: 55 0.239 - 0.319: 6 0.319 - 0.398: 2 Chirality restraints: 4447 Sorted by residual: chirality pdb=" CB ILE e 23 " pdb=" CA ILE e 23 " pdb=" CG1 ILE e 23 " pdb=" CG2 ILE e 23 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.97e+00 chirality pdb=" CA ARG B 355 " pdb=" N ARG B 355 " pdb=" C ARG B 355 " pdb=" CB ARG B 355 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CB ILE D 189 " pdb=" CA ILE D 189 " pdb=" CG1 ILE D 189 " pdb=" CG2 ILE D 189 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 4444 not shown) Planarity restraints: 4912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR e 9 " 0.053 5.00e-02 4.00e+02 8.00e-02 1.02e+01 pdb=" N PRO e 10 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO e 10 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO e 10 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 295 " -0.014 2.00e-02 2.50e+03 2.86e-02 8.18e+00 pdb=" C ALA D 295 " 0.049 2.00e-02 2.50e+03 pdb=" O ALA D 295 " -0.019 2.00e-02 2.50e+03 pdb=" N VAL D 296 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA D 338 " 0.047 5.00e-02 4.00e+02 7.08e-02 8.01e+00 pdb=" N PRO D 339 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO D 339 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 339 " 0.040 5.00e-02 4.00e+02 ... (remaining 4909 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 3132 2.73 - 3.27: 29511 3.27 - 3.82: 50039 3.82 - 4.36: 56118 4.36 - 4.90: 91268 Nonbonded interactions: 230068 Sorted by model distance: nonbonded pdb=" OG1 THR B 177 " pdb=" O2B ATP B 600 " model vdw 2.192 3.040 nonbonded pdb=" O LEU D 47 " pdb=" OG1 THR D 62 " model vdw 2.202 3.040 nonbonded pdb=" O ASP F 366 " pdb=" OG SER F 370 " model vdw 2.220 3.040 nonbonded pdb=" OG1 THR D 179 " pdb=" O1G ATP D 601 " model vdw 2.227 3.040 nonbonded pdb=" O VAL D 102 " pdb=" OG1 THR D 128 " model vdw 2.236 3.040 ... (remaining 230063 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 503 or resid 600)) selection = (chain 'B' and resid 6 through 600) selection = (chain 'C' and (resid 6 through 503 or resid 600)) } ncs_group { reference = (chain 'D' and resid 17 through 494) selection = (chain 'E' and resid 17 through 494) selection = (chain 'F' and resid 17 through 494) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 24.820 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.089 27884 Z= 0.408 Angle : 1.159 25.129 37788 Z= 0.697 Chirality : 0.060 0.398 4447 Planarity : 0.007 0.080 4912 Dihedral : 16.431 111.745 10481 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.12 % Favored : 89.74 % Rotamer: Outliers : 0.78 % Allowed : 15.57 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.98 (0.12), residues: 3558 helix: -2.19 (0.11), residues: 1441 sheet: -2.82 (0.20), residues: 466 loop : -2.96 (0.13), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 277 TYR 0.021 0.003 TYR A 464 PHE 0.030 0.003 PHE E 430 TRP 0.005 0.001 TRP e 15 HIS 0.013 0.002 HIS B 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00798 / 0.41 (27883) covalent geometry : angle 1.15875 / 0.70 (37786) SS BOND : bond 0.00667 / 0.35 ( 1) SS BOND : angle 2.83779 / 1.89 ( 2) hydrogen bonds : bond 0.15973 / 11.15 ( 1236) hydrogen bonds : angle 7.23655 / 5.06 ( 3687) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 315 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.8908 (tp) cc_final: 0.8222 (mt) REVERT: A 157 MET cc_start: 0.8592 (ptp) cc_final: 0.7921 (mmt) REVERT: A 276 LEU cc_start: 0.9172 (tp) cc_final: 0.8939 (tp) REVERT: A 314 MET cc_start: 0.8101 (mmm) cc_final: 0.7579 (mmm) REVERT: A 338 ILE cc_start: 0.9350 (mm) cc_final: 0.9111 (mt) REVERT: A 351 ASN cc_start: 0.8598 (t0) cc_final: 0.8190 (t0) REVERT: A 376 MET cc_start: 0.8789 (tpp) cc_final: 0.8509 (mmp) REVERT: A 436 MET cc_start: 0.8677 (ptp) cc_final: 0.8099 (ptp) REVERT: A 498 MET cc_start: 0.8896 (ttm) cc_final: 0.8511 (mtp) REVERT: B 236 GLN cc_start: 0.9148 (mt0) cc_final: 0.8910 (mt0) REVERT: B 251 MET cc_start: 0.7596 (tpt) cc_final: 0.7009 (tpt) REVERT: B 314 MET cc_start: 0.7909 (tpt) cc_final: 0.6968 (tpt) REVERT: B 323 GLN cc_start: 0.8614 (mp-120) cc_final: 0.8312 (mm110) REVERT: C 235 LEU cc_start: 0.9417 (mt) cc_final: 0.9201 (mt) REVERT: C 474 GLU cc_start: 0.9100 (mm-30) cc_final: 0.8889 (mm-30) REVERT: D 256 MET cc_start: 0.8680 (mmt) cc_final: 0.8413 (mmp) REVERT: D 488 MET cc_start: 0.9184 (tmm) cc_final: 0.8928 (tmm) REVERT: E 79 MET cc_start: 0.9180 (mmt) cc_final: 0.8940 (mmp) REVERT: E 239 MET cc_start: 0.8625 (mmm) cc_final: 0.8195 (mmm) REVERT: E 247 MET cc_start: 0.8686 (tpp) cc_final: 0.8423 (tpp) REVERT: F 79 MET cc_start: 0.8503 (mpp) cc_final: 0.8029 (mpp) REVERT: F 89 MET cc_start: 0.8623 (ttm) cc_final: 0.8314 (mtp) REVERT: d 139 GLN cc_start: 0.9279 (mm110) cc_final: 0.8964 (mp10) REVERT: d 250 MET cc_start: 0.4386 (mmt) cc_final: 0.3183 (mtm) REVERT: g 62 GLU cc_start: 0.8987 (tm-30) cc_final: 0.8729 (tm-30) REVERT: g 66 LEU cc_start: 0.8732 (mt) cc_final: 0.8095 (tt) REVERT: g 133 PHE cc_start: 0.8726 (t80) cc_final: 0.8383 (t80) REVERT: g 346 GLN cc_start: 0.8521 (mm110) cc_final: 0.8038 (mt0) outliers start: 23 outliers final: 12 residues processed: 335 average time/residue: 0.1755 time to fit residues: 95.8188 Evaluate side-chains 224 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 212 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 ASN A 495 GLN B 66 ASN B 148 GLN B 186 ASN B 269 GLN B 295 HIS B 359 ASN C 34 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 GLN C 423 GLN C 434 GLN C 468 ASN D 19 ASN ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN D 133 HIS D 299 GLN E 25 GLN E 120 ASN E 402 GLN E 472 GLN F 19 ASN F 193 HIS F 225 GLN F 264 ASN F 389 GLN F 402 GLN ** d 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 147 ASN d 247 GLN e 56 GLN g 81 ASN g 95 ASN g 97 ASN g 192 GLN g 228 HIS ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.049826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.040984 restraints weight = 190954.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.042311 restraints weight = 116367.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.043270 restraints weight = 79157.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.043947 restraints weight = 58476.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.044430 restraints weight = 46140.751| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27884 Z= 0.152 Angle : 0.711 9.583 37788 Z= 0.370 Chirality : 0.046 0.204 4447 Planarity : 0.005 0.064 4912 Dihedral : 7.591 102.681 3899 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.23 % Favored : 91.62 % Rotamer: Outliers : 0.17 % Allowed : 5.17 % Favored : 94.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.13), residues: 3558 helix: -0.90 (0.12), residues: 1460 sheet: -2.33 (0.21), residues: 460 loop : -2.67 (0.14), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 455 TYR 0.017 0.001 TYR D 362 PHE 0.027 0.001 PHE C 482 TRP 0.004 0.001 TRP e 15 HIS 0.004 0.001 HIS D 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 (27883) covalent geometry : angle 0.71068 / 0.37 (37786) SS BOND : bond 0.00319 / 0.17 ( 1) SS BOND : angle 2.25489 / 1.50 ( 2) hydrogen bonds : bond 0.04691 / 3.21 ( 1236) hydrogen bonds : angle 5.65401 / 3.97 ( 3687) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 315 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.8958 (tp) cc_final: 0.8587 (tp) REVERT: A 157 MET cc_start: 0.9021 (ptp) cc_final: 0.7963 (mmt) REVERT: A 251 MET cc_start: 0.8269 (ptp) cc_final: 0.7756 (ppp) REVERT: A 314 MET cc_start: 0.8155 (mmm) cc_final: 0.7767 (mmm) REVERT: B 82 MET cc_start: 0.8736 (mmp) cc_final: 0.8534 (mmp) REVERT: B 131 GLU cc_start: 0.8828 (mp0) cc_final: 0.8454 (tp30) REVERT: B 236 GLN cc_start: 0.9212 (mt0) cc_final: 0.8706 (mm-40) REVERT: B 355 ARG cc_start: 0.9057 (mmp-170) cc_final: 0.8209 (mmm160) REVERT: C 182 ASP cc_start: 0.8237 (m-30) cc_final: 0.7987 (m-30) REVERT: C 251 MET cc_start: 0.8878 (ttt) cc_final: 0.8615 (ttt) REVERT: C 295 HIS cc_start: 0.8945 (m-70) cc_final: 0.8736 (m-70) REVERT: D 64 GLU cc_start: 0.5834 (tp30) cc_final: 0.5310 (tp30) REVERT: D 183 MET cc_start: 0.9040 (mmp) cc_final: 0.8707 (mmm) REVERT: D 256 MET cc_start: 0.8883 (mmt) cc_final: 0.8611 (mmp) REVERT: D 488 MET cc_start: 0.9221 (tmm) cc_final: 0.8911 (tmm) REVERT: E 79 MET cc_start: 0.9293 (mmt) cc_final: 0.8909 (mmp) REVERT: E 239 MET cc_start: 0.8771 (mmm) cc_final: 0.8455 (mmm) REVERT: E 247 MET cc_start: 0.8718 (tpp) cc_final: 0.8414 (tpp) REVERT: F 79 MET cc_start: 0.8630 (mpp) cc_final: 0.7870 (mpp) REVERT: d 139 GLN cc_start: 0.9343 (mm110) cc_final: 0.9069 (mp10) REVERT: d 250 MET cc_start: 0.4443 (mmt) cc_final: 0.3542 (mtm) REVERT: e 95 THR cc_start: 0.8850 (t) cc_final: 0.8463 (p) REVERT: e 127 GLU cc_start: 0.7363 (tm-30) cc_final: 0.6883 (tp30) REVERT: g 62 GLU cc_start: 0.9134 (tm-30) cc_final: 0.8894 (tm-30) REVERT: g 66 LEU cc_start: 0.8431 (mt) cc_final: 0.8016 (tt) REVERT: g 133 PHE cc_start: 0.8514 (t80) cc_final: 0.8169 (t80) REVERT: g 295 LEU cc_start: 0.9348 (mt) cc_final: 0.9120 (mt) REVERT: g 346 GLN cc_start: 0.8521 (mm110) cc_final: 0.7928 (mt0) outliers start: 5 outliers final: 1 residues processed: 319 average time/residue: 0.1854 time to fit residues: 94.6570 Evaluate side-chains 212 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 211 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 216 optimal weight: 2.9990 chunk 277 optimal weight: 1.9990 chunk 222 optimal weight: 7.9990 chunk 266 optimal weight: 7.9990 chunk 313 optimal weight: 0.9980 chunk 263 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 247 optimal weight: 0.5980 chunk 41 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 GLN ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 GLN ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN ** D 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 GLN ** F 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 238 GLN ** d 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.049066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.040432 restraints weight = 188913.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.041712 restraints weight = 115264.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.042625 restraints weight = 78860.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.043282 restraints weight = 58186.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.043783 restraints weight = 45876.878| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 27884 Z= 0.178 Angle : 0.697 9.482 37788 Z= 0.364 Chirality : 0.045 0.201 4447 Planarity : 0.005 0.070 4912 Dihedral : 7.320 100.467 3899 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.74 % Favored : 91.12 % Rotamer: Outliers : 0.03 % Allowed : 5.51 % Favored : 94.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.13), residues: 3558 helix: -0.37 (0.13), residues: 1459 sheet: -2.05 (0.23), residues: 455 loop : -2.45 (0.14), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 277 TYR 0.017 0.002 TYR C 330 PHE 0.045 0.002 PHE B 213 TRP 0.002 0.001 TRP e 57 HIS 0.003 0.001 HIS D 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.18 (27883) covalent geometry : angle 0.69712 / 0.36 (37786) SS BOND : bond 0.00297 / 0.16 ( 1) SS BOND : angle 2.35412 / 1.57 ( 2) hydrogen bonds : bond 0.04420 / 3.04 ( 1236) hydrogen bonds : angle 5.42957 / 3.79 ( 3687) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 276 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.9317 (pmm) cc_final: 0.9114 (pmm) REVERT: A 147 LEU cc_start: 0.8943 (tp) cc_final: 0.8590 (tp) REVERT: A 157 MET cc_start: 0.8923 (ptp) cc_final: 0.7946 (mmt) REVERT: A 251 MET cc_start: 0.8117 (ptp) cc_final: 0.7601 (ppp) REVERT: A 314 MET cc_start: 0.8238 (mmm) cc_final: 0.7814 (mmm) REVERT: A 498 MET cc_start: 0.8849 (mtm) cc_final: 0.8196 (mtp) REVERT: B 82 MET cc_start: 0.8704 (mmp) cc_final: 0.8489 (mmp) REVERT: B 131 GLU cc_start: 0.8745 (mp0) cc_final: 0.8432 (tp30) REVERT: B 236 GLN cc_start: 0.9236 (mt0) cc_final: 0.8819 (mm-40) REVERT: B 251 MET cc_start: 0.7373 (tpt) cc_final: 0.6799 (tpt) REVERT: B 314 MET cc_start: 0.8071 (tpt) cc_final: 0.7443 (tpt) REVERT: C 77 MET cc_start: 0.8290 (mtp) cc_final: 0.8049 (mtp) REVERT: C 182 ASP cc_start: 0.8184 (m-30) cc_final: 0.7978 (m-30) REVERT: C 235 LEU cc_start: 0.9414 (mt) cc_final: 0.9178 (mt) REVERT: C 251 MET cc_start: 0.8923 (ttt) cc_final: 0.8575 (ttt) REVERT: C 295 HIS cc_start: 0.8907 (m-70) cc_final: 0.8681 (m-70) REVERT: D 64 GLU cc_start: 0.5838 (tp30) cc_final: 0.5364 (tp30) REVERT: D 183 MET cc_start: 0.8874 (mmp) cc_final: 0.8643 (mmm) REVERT: D 214 MET cc_start: 0.8765 (tmm) cc_final: 0.8556 (tmm) REVERT: D 488 MET cc_start: 0.9193 (tmm) cc_final: 0.8905 (tmm) REVERT: E 79 MET cc_start: 0.9275 (mmt) cc_final: 0.8918 (mmp) REVERT: E 247 MET cc_start: 0.8666 (tpp) cc_final: 0.8410 (tpp) REVERT: F 79 MET cc_start: 0.8724 (mpp) cc_final: 0.7915 (mpp) REVERT: d 139 GLN cc_start: 0.9335 (mm110) cc_final: 0.9045 (mp10) REVERT: d 250 MET cc_start: 0.4387 (mmt) cc_final: 0.3578 (mtm) REVERT: g 66 LEU cc_start: 0.8457 (mt) cc_final: 0.7916 (tt) REVERT: g 133 PHE cc_start: 0.8516 (t80) cc_final: 0.8241 (t80) REVERT: g 284 PHE cc_start: 0.8411 (m-10) cc_final: 0.8088 (m-10) REVERT: g 295 LEU cc_start: 0.9353 (mt) cc_final: 0.9025 (mt) REVERT: g 346 GLN cc_start: 0.8535 (mm110) cc_final: 0.7930 (mt0) outliers start: 1 outliers final: 0 residues processed: 276 average time/residue: 0.1715 time to fit residues: 78.3276 Evaluate side-chains 193 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 242 optimal weight: 5.9990 chunk 213 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 187 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 chunk 308 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 288 optimal weight: 0.8980 chunk 97 optimal weight: 0.0980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 GLN B 351 ASN C 34 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN ** D 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 GLN ** F 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 72 ASN ** g 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 346 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.049976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.041156 restraints weight = 189415.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.042468 restraints weight = 115913.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.043403 restraints weight = 79331.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.044108 restraints weight = 58730.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.044566 restraints weight = 46217.480| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27884 Z= 0.141 Angle : 0.663 10.213 37788 Z= 0.344 Chirality : 0.045 0.240 4447 Planarity : 0.005 0.052 4912 Dihedral : 7.053 97.527 3899 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.84 % Favored : 92.07 % Rotamer: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.14), residues: 3558 helix: -0.03 (0.13), residues: 1448 sheet: -1.89 (0.23), residues: 472 loop : -2.27 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 462 TYR 0.027 0.001 TYR B 457 PHE 0.032 0.001 PHE B 213 TRP 0.006 0.001 TRP e 15 HIS 0.004 0.001 HIS E 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (27883) covalent geometry : angle 0.66301 / 0.34 (37786) SS BOND : bond 0.00295 / 0.16 ( 1) SS BOND : angle 2.41220 / 1.61 ( 2) hydrogen bonds : bond 0.04095 / 2.81 ( 1236) hydrogen bonds : angle 5.18227 / 3.62 ( 3687) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.9019 (tp) cc_final: 0.8657 (tp) REVERT: A 157 MET cc_start: 0.8974 (ptp) cc_final: 0.8032 (mmt) REVERT: A 251 MET cc_start: 0.8182 (ptp) cc_final: 0.7748 (ppp) REVERT: A 314 MET cc_start: 0.8313 (mmm) cc_final: 0.7801 (mmm) REVERT: A 326 ASP cc_start: 0.9507 (m-30) cc_final: 0.9246 (m-30) REVERT: A 498 MET cc_start: 0.8764 (mtm) cc_final: 0.8140 (mtp) REVERT: B 82 MET cc_start: 0.8768 (mmp) cc_final: 0.8551 (mmp) REVERT: B 131 GLU cc_start: 0.8777 (mp0) cc_final: 0.8467 (tp30) REVERT: B 236 GLN cc_start: 0.9264 (mt0) cc_final: 0.8834 (mm-40) REVERT: B 251 MET cc_start: 0.7440 (tpt) cc_final: 0.6852 (tpt) REVERT: B 314 MET cc_start: 0.8179 (tpt) cc_final: 0.7491 (tpt) REVERT: C 235 LEU cc_start: 0.9409 (mt) cc_final: 0.9185 (mt) REVERT: C 251 MET cc_start: 0.8894 (ttt) cc_final: 0.8607 (ttt) REVERT: C 295 HIS cc_start: 0.8869 (m-70) cc_final: 0.8619 (m-70) REVERT: D 44 TYR cc_start: 0.8825 (m-80) cc_final: 0.7974 (m-80) REVERT: D 89 MET cc_start: 0.7863 (mtm) cc_final: 0.7348 (mtp) REVERT: D 333 ASP cc_start: 0.8852 (t0) cc_final: 0.8569 (t70) REVERT: D 488 MET cc_start: 0.9206 (tmm) cc_final: 0.8920 (tmm) REVERT: E 79 MET cc_start: 0.9181 (mmt) cc_final: 0.8812 (mmp) REVERT: E 89 MET cc_start: 0.8249 (tpt) cc_final: 0.8025 (tpt) REVERT: F 79 MET cc_start: 0.8836 (mpp) cc_final: 0.7993 (mpp) REVERT: d 250 MET cc_start: 0.4696 (mmt) cc_final: 0.3540 (mtm) REVERT: g 66 LEU cc_start: 0.8563 (mt) cc_final: 0.7826 (tt) REVERT: g 133 PHE cc_start: 0.8432 (t80) cc_final: 0.8207 (t80) REVERT: g 295 LEU cc_start: 0.9350 (mt) cc_final: 0.9048 (mt) REVERT: g 346 GLN cc_start: 0.8461 (mm-40) cc_final: 0.7958 (mt0) outliers start: 0 outliers final: 0 residues processed: 289 average time/residue: 0.1736 time to fit residues: 82.8356 Evaluate side-chains 203 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 176 optimal weight: 0.6980 chunk 175 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 281 optimal weight: 1.9990 chunk 306 optimal weight: 0.0570 chunk 66 optimal weight: 9.9990 chunk 318 optimal weight: 9.9990 chunk 297 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 330 optimal weight: 6.9990 chunk 248 optimal weight: 4.9990 overall best weight: 1.9504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 HIS B 164 GLN B 389 GLN C 34 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN D 299 GLN ** E 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.049812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.041074 restraints weight = 192529.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.042355 restraints weight = 118338.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.043299 restraints weight = 81275.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.043975 restraints weight = 60111.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.044447 restraints weight = 47521.165| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27884 Z= 0.156 Angle : 0.666 10.260 37788 Z= 0.346 Chirality : 0.045 0.199 4447 Planarity : 0.005 0.051 4912 Dihedral : 6.941 98.580 3899 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.21 % Favored : 91.71 % Rotamer: Outliers : 0.03 % Allowed : 3.98 % Favored : 95.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.14), residues: 3558 helix: 0.12 (0.13), residues: 1450 sheet: -1.84 (0.23), residues: 478 loop : -2.13 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 141 TYR 0.018 0.001 TYR B 457 PHE 0.027 0.002 PHE B 213 TRP 0.004 0.001 TRP e 57 HIS 0.008 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 (27883) covalent geometry : angle 0.66628 / 0.35 (37786) SS BOND : bond 0.00279 / 0.15 ( 1) SS BOND : angle 2.35705 / 1.57 ( 2) hydrogen bonds : bond 0.04055 / 2.80 ( 1236) hydrogen bonds : angle 5.10575 / 3.56 ( 3687) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 276 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.9009 (tp) cc_final: 0.8639 (tp) REVERT: A 157 MET cc_start: 0.8922 (ptp) cc_final: 0.7976 (mmt) REVERT: A 251 MET cc_start: 0.8188 (ptp) cc_final: 0.7787 (ppp) REVERT: A 314 MET cc_start: 0.8292 (mmm) cc_final: 0.7722 (mmm) REVERT: A 498 MET cc_start: 0.8724 (mtm) cc_final: 0.8081 (mtp) REVERT: B 82 MET cc_start: 0.8768 (mmp) cc_final: 0.8554 (mmp) REVERT: B 131 GLU cc_start: 0.8760 (mp0) cc_final: 0.8531 (tp30) REVERT: B 236 GLN cc_start: 0.9311 (mt0) cc_final: 0.8799 (mm-40) REVERT: B 251 MET cc_start: 0.7519 (tpt) cc_final: 0.6893 (tpt) REVERT: B 314 MET cc_start: 0.8235 (tpt) cc_final: 0.7488 (tpt) REVERT: C 235 LEU cc_start: 0.9413 (mt) cc_final: 0.9185 (mt) REVERT: C 251 MET cc_start: 0.8902 (ttt) cc_final: 0.8599 (ttt) REVERT: C 295 HIS cc_start: 0.8981 (m-70) cc_final: 0.8711 (m-70) REVERT: D 488 MET cc_start: 0.9210 (tmm) cc_final: 0.8917 (tmm) REVERT: E 59 MET cc_start: 0.8630 (ptp) cc_final: 0.8296 (ptp) REVERT: E 79 MET cc_start: 0.9072 (mmt) cc_final: 0.8741 (mmp) REVERT: E 89 MET cc_start: 0.8124 (tpt) cc_final: 0.7847 (tpt) REVERT: E 162 TYR cc_start: 0.7840 (m-80) cc_final: 0.7613 (m-10) REVERT: E 247 MET cc_start: 0.8883 (tpt) cc_final: 0.8490 (tpp) REVERT: E 273 ASP cc_start: 0.8676 (t0) cc_final: 0.8420 (t70) REVERT: F 79 MET cc_start: 0.8842 (mpp) cc_final: 0.7973 (mpp) REVERT: F 167 LYS cc_start: 0.9224 (mppt) cc_final: 0.8925 (mtmt) REVERT: d 250 MET cc_start: 0.4623 (mmt) cc_final: 0.3606 (mtm) REVERT: g 66 LEU cc_start: 0.8284 (mt) cc_final: 0.7805 (tt) REVERT: g 272 LYS cc_start: 0.7832 (tppt) cc_final: 0.7344 (tppt) REVERT: g 282 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7521 (pp) REVERT: g 295 LEU cc_start: 0.9244 (mt) cc_final: 0.8825 (mt) REVERT: g 346 GLN cc_start: 0.8486 (mm-40) cc_final: 0.7903 (mt0) outliers start: 1 outliers final: 0 residues processed: 277 average time/residue: 0.1718 time to fit residues: 79.4622 Evaluate side-chains 198 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 197 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 174 optimal weight: 0.8980 chunk 326 optimal weight: 3.9990 chunk 220 optimal weight: 2.9990 chunk 330 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 150 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 221 optimal weight: 1.9990 chunk 260 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 ASN B 43 HIS B 164 GLN B 269 GLN C 34 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN D 299 GLN ** E 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.049505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.040775 restraints weight = 193108.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.042038 restraints weight = 118844.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.042954 restraints weight = 81968.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.043616 restraints weight = 61066.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.044129 restraints weight = 48362.139| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 27884 Z= 0.171 Angle : 0.679 10.601 37788 Z= 0.350 Chirality : 0.045 0.193 4447 Planarity : 0.005 0.053 4912 Dihedral : 6.906 99.215 3899 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.32 % Favored : 91.60 % Rotamer: Outliers : 0.10 % Allowed : 3.13 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.14), residues: 3558 helix: 0.25 (0.13), residues: 1447 sheet: -1.72 (0.23), residues: 482 loop : -2.08 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 366 TYR 0.016 0.002 TYR B 457 PHE 0.028 0.002 PHE g 133 TRP 0.007 0.001 TRP e 57 HIS 0.013 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (27883) covalent geometry : angle 0.67831 / 0.35 (37786) SS BOND : bond 0.00356 / 0.19 ( 1) SS BOND : angle 3.06361 / 2.04 ( 2) hydrogen bonds : bond 0.04054 / 2.80 ( 1236) hydrogen bonds : angle 5.02765 / 3.50 ( 3687) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 267 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.9003 (tp) cc_final: 0.8619 (tp) REVERT: A 157 MET cc_start: 0.8877 (ptp) cc_final: 0.7939 (mmt) REVERT: A 219 MET cc_start: 0.9153 (mmm) cc_final: 0.8944 (mmm) REVERT: A 251 MET cc_start: 0.8179 (ptp) cc_final: 0.7798 (ppp) REVERT: A 274 MET cc_start: 0.8410 (ptp) cc_final: 0.8135 (mtt) REVERT: A 314 MET cc_start: 0.8358 (mmm) cc_final: 0.7834 (mmm) REVERT: A 498 MET cc_start: 0.8674 (mtm) cc_final: 0.8001 (mtp) REVERT: B 1 MET cc_start: 0.5853 (mmt) cc_final: 0.5562 (mmt) REVERT: B 236 GLN cc_start: 0.9287 (mt0) cc_final: 0.8770 (mm-40) REVERT: B 251 MET cc_start: 0.7525 (tpt) cc_final: 0.6963 (tpt) REVERT: B 276 LEU cc_start: 0.9100 (tp) cc_final: 0.8316 (tp) REVERT: B 314 MET cc_start: 0.8274 (tpt) cc_final: 0.7548 (tpt) REVERT: C 77 MET cc_start: 0.8232 (mtp) cc_final: 0.7963 (mtp) REVERT: C 235 LEU cc_start: 0.9413 (mt) cc_final: 0.9158 (mt) REVERT: C 251 MET cc_start: 0.8861 (ttt) cc_final: 0.8496 (ttt) REVERT: C 295 HIS cc_start: 0.8940 (m-70) cc_final: 0.8650 (m-70) REVERT: D 183 MET cc_start: 0.8838 (mmp) cc_final: 0.8557 (mmm) REVERT: D 488 MET cc_start: 0.9184 (tmm) cc_final: 0.8957 (tmm) REVERT: E 79 MET cc_start: 0.9075 (mmt) cc_final: 0.8722 (mmp) REVERT: E 89 MET cc_start: 0.8084 (tpt) cc_final: 0.7808 (tpt) REVERT: E 247 MET cc_start: 0.8870 (tpt) cc_final: 0.8432 (tpp) REVERT: E 273 ASP cc_start: 0.8791 (t0) cc_final: 0.8532 (t70) REVERT: E 335 THR cc_start: 0.8744 (t) cc_final: 0.7910 (t) REVERT: E 374 MET cc_start: 0.8516 (mmm) cc_final: 0.8046 (mmm) REVERT: F 79 MET cc_start: 0.8910 (mpp) cc_final: 0.7977 (mpp) REVERT: F 167 LYS cc_start: 0.9246 (mppt) cc_final: 0.8941 (mtmt) REVERT: d 250 MET cc_start: 0.4696 (mmt) cc_final: 0.3717 (mtm) REVERT: e 90 GLN cc_start: 0.9395 (tm-30) cc_final: 0.9193 (tm-30) REVERT: g 66 LEU cc_start: 0.8523 (mt) cc_final: 0.7777 (tt) REVERT: g 295 LEU cc_start: 0.9356 (mt) cc_final: 0.9068 (mt) REVERT: g 323 MET cc_start: 0.9412 (mmp) cc_final: 0.8924 (mmm) REVERT: g 346 GLN cc_start: 0.8505 (mm-40) cc_final: 0.7944 (mt0) outliers start: 3 outliers final: 1 residues processed: 270 average time/residue: 0.1703 time to fit residues: 76.9703 Evaluate side-chains 208 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 207 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 71 optimal weight: 0.9990 chunk 175 optimal weight: 5.9990 chunk 243 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 59 optimal weight: 0.3980 chunk 190 optimal weight: 4.9990 chunk 147 optimal weight: 7.9990 chunk 281 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 349 optimal weight: 1.9990 chunk 276 optimal weight: 0.0670 overall best weight: 0.8924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 GLN ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 HIS B 164 GLN C 34 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN ** E 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 ASN ** d 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.051017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.042128 restraints weight = 187992.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.043439 restraints weight = 116120.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.044401 restraints weight = 80043.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.045048 restraints weight = 59502.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.045595 restraints weight = 47198.784| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27884 Z= 0.123 Angle : 0.668 11.484 37788 Z= 0.339 Chirality : 0.045 0.197 4447 Planarity : 0.004 0.054 4912 Dihedral : 6.725 94.899 3899 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.56 % Favored : 92.36 % Rotamer: Outliers : 0.03 % Allowed : 2.04 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.14), residues: 3558 helix: 0.36 (0.13), residues: 1456 sheet: -1.55 (0.24), residues: 471 loop : -2.03 (0.15), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 500 TYR 0.018 0.001 TYR g 167 PHE 0.025 0.001 PHE g 168 TRP 0.007 0.001 TRP e 57 HIS 0.010 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (27883) covalent geometry : angle 0.66752 / 0.34 (37786) SS BOND : bond 0.00566 / 0.30 ( 1) SS BOND : angle 2.46834 / 1.65 ( 2) hydrogen bonds : bond 0.03822 / 2.63 ( 1236) hydrogen bonds : angle 4.87357 / 3.40 ( 3687) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 287 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.9081 (tp) cc_final: 0.8753 (tp) REVERT: A 157 MET cc_start: 0.8820 (ptp) cc_final: 0.7917 (mmt) REVERT: A 219 MET cc_start: 0.9153 (mmm) cc_final: 0.8922 (mmm) REVERT: A 251 MET cc_start: 0.8195 (ptp) cc_final: 0.7909 (ppp) REVERT: A 274 MET cc_start: 0.8411 (ptp) cc_final: 0.8002 (mtp) REVERT: A 314 MET cc_start: 0.8323 (mmm) cc_final: 0.7730 (mmm) REVERT: A 376 MET cc_start: 0.9030 (ptt) cc_final: 0.8475 (ppp) REVERT: A 498 MET cc_start: 0.8695 (mtm) cc_final: 0.8076 (mtp) REVERT: B 1 MET cc_start: 0.5692 (mmt) cc_final: 0.5398 (mmt) REVERT: B 236 GLN cc_start: 0.9312 (mt0) cc_final: 0.8798 (mm-40) REVERT: B 355 ARG cc_start: 0.8896 (mmp-170) cc_final: 0.8500 (mmm160) REVERT: C 77 MET cc_start: 0.8177 (mtp) cc_final: 0.7857 (mtp) REVERT: C 182 ASP cc_start: 0.8030 (m-30) cc_final: 0.7823 (m-30) REVERT: C 234 THR cc_start: 0.9202 (p) cc_final: 0.8990 (p) REVERT: C 235 LEU cc_start: 0.9362 (mt) cc_final: 0.9151 (mt) REVERT: C 251 MET cc_start: 0.8826 (ttt) cc_final: 0.8518 (ttt) REVERT: C 295 HIS cc_start: 0.8890 (m-70) cc_final: 0.8579 (m-70) REVERT: C 403 LEU cc_start: 0.9417 (mm) cc_final: 0.9066 (mt) REVERT: D 59 MET cc_start: 0.6958 (tmm) cc_final: 0.6690 (tmm) REVERT: D 79 MET cc_start: 0.8563 (ttp) cc_final: 0.8223 (ttp) REVERT: D 183 MET cc_start: 0.8791 (mmp) cc_final: 0.8514 (mmm) REVERT: D 247 MET cc_start: 0.8731 (ttt) cc_final: 0.8496 (ttm) REVERT: D 488 MET cc_start: 0.9184 (tmm) cc_final: 0.8968 (tmm) REVERT: E 59 MET cc_start: 0.8561 (ptp) cc_final: 0.8169 (ptp) REVERT: E 79 MET cc_start: 0.9097 (mmt) cc_final: 0.8798 (mmp) REVERT: E 89 MET cc_start: 0.7941 (tpt) cc_final: 0.7619 (tpt) REVERT: E 247 MET cc_start: 0.8808 (tpt) cc_final: 0.8407 (tpp) REVERT: E 306 MET cc_start: 0.9050 (tpp) cc_final: 0.8718 (mmm) REVERT: E 335 THR cc_start: 0.8659 (t) cc_final: 0.7895 (t) REVERT: E 374 MET cc_start: 0.8581 (mmm) cc_final: 0.8275 (mtp) REVERT: F 167 LYS cc_start: 0.9208 (mppt) cc_final: 0.8888 (mtmt) REVERT: F 256 MET cc_start: 0.8572 (mmm) cc_final: 0.8014 (mmm) REVERT: d 250 MET cc_start: 0.4834 (mmt) cc_final: 0.3899 (mtm) REVERT: e 109 LYS cc_start: 0.9460 (ttpp) cc_final: 0.8988 (tppt) REVERT: g 66 LEU cc_start: 0.8560 (mt) cc_final: 0.7880 (tt) REVERT: g 133 PHE cc_start: 0.8490 (t80) cc_final: 0.8113 (t80) REVERT: g 272 LYS cc_start: 0.8186 (tppt) cc_final: 0.7810 (tppt) REVERT: g 323 MET cc_start: 0.9349 (mmp) cc_final: 0.8900 (mmm) REVERT: g 346 GLN cc_start: 0.8381 (mm-40) cc_final: 0.7929 (mt0) outliers start: 1 outliers final: 0 residues processed: 288 average time/residue: 0.1688 time to fit residues: 81.0511 Evaluate side-chains 217 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 332 optimal weight: 4.9990 chunk 329 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 307 optimal weight: 7.9990 chunk 287 optimal weight: 0.0040 chunk 246 optimal weight: 2.9990 chunk 32 optimal weight: 0.0020 chunk 123 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 267 optimal weight: 1.9990 overall best weight: 0.9404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 HIS B 164 GLN B 269 GLN C 34 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN D 67 GLN ** E 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.050926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.041984 restraints weight = 190419.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.043321 restraints weight = 117048.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.044295 restraints weight = 80321.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.044994 restraints weight = 59481.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.045514 restraints weight = 46895.886| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27884 Z= 0.123 Angle : 0.654 11.731 37788 Z= 0.333 Chirality : 0.045 0.196 4447 Planarity : 0.004 0.055 4912 Dihedral : 6.603 93.990 3899 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.42 % Favored : 92.50 % Rotamer: Outliers : 0.03 % Allowed : 1.22 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.14), residues: 3558 helix: 0.47 (0.13), residues: 1464 sheet: -1.51 (0.24), residues: 483 loop : -2.00 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG g 256 TYR 0.020 0.001 TYR C 241 PHE 0.017 0.001 PHE E 271 TRP 0.006 0.001 TRP e 57 HIS 0.009 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (27883) covalent geometry : angle 0.65377 / 0.33 (37786) SS BOND : bond 0.00485 / 0.26 ( 1) SS BOND : angle 2.04554 / 1.36 ( 2) hydrogen bonds : bond 0.03767 / 2.61 ( 1236) hydrogen bonds : angle 4.78936 / 3.35 ( 3687) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 280 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.9063 (tp) cc_final: 0.8766 (tp) REVERT: A 157 MET cc_start: 0.8818 (ptp) cc_final: 0.7917 (mmt) REVERT: A 219 MET cc_start: 0.9135 (mmm) cc_final: 0.8873 (mmm) REVERT: A 251 MET cc_start: 0.8181 (ptp) cc_final: 0.7915 (ppp) REVERT: A 274 MET cc_start: 0.8545 (ptp) cc_final: 0.8083 (mtp) REVERT: A 314 MET cc_start: 0.8354 (mmm) cc_final: 0.7704 (mmm) REVERT: A 498 MET cc_start: 0.8758 (mtm) cc_final: 0.8247 (mtp) REVERT: B 1 MET cc_start: 0.5718 (mmt) cc_final: 0.5513 (mmt) REVERT: B 236 GLN cc_start: 0.9380 (mt0) cc_final: 0.9067 (mt0) REVERT: B 251 MET cc_start: 0.7300 (tpt) cc_final: 0.6549 (tpt) REVERT: B 314 MET cc_start: 0.8206 (tpt) cc_final: 0.7726 (tpt) REVERT: B 355 ARG cc_start: 0.8905 (mmp-170) cc_final: 0.8317 (mmm160) REVERT: C 77 MET cc_start: 0.8173 (mtp) cc_final: 0.7912 (mtp) REVERT: C 234 THR cc_start: 0.9197 (p) cc_final: 0.8996 (p) REVERT: C 235 LEU cc_start: 0.9419 (mt) cc_final: 0.9199 (mt) REVERT: C 251 MET cc_start: 0.8705 (ttt) cc_final: 0.8465 (ttt) REVERT: C 295 HIS cc_start: 0.8933 (m-70) cc_final: 0.8671 (m-70) REVERT: D 183 MET cc_start: 0.8778 (mmp) cc_final: 0.8515 (mmm) REVERT: D 247 MET cc_start: 0.8663 (ttt) cc_final: 0.8388 (ttm) REVERT: D 488 MET cc_start: 0.9165 (tmm) cc_final: 0.8943 (tmm) REVERT: E 79 MET cc_start: 0.9056 (mmt) cc_final: 0.8785 (mmp) REVERT: E 89 MET cc_start: 0.8027 (tpt) cc_final: 0.7685 (tpt) REVERT: E 214 MET cc_start: 0.9265 (mmp) cc_final: 0.9037 (mmm) REVERT: E 247 MET cc_start: 0.8821 (tpt) cc_final: 0.8415 (tpp) REVERT: E 273 ASP cc_start: 0.8646 (t0) cc_final: 0.8443 (t70) REVERT: E 306 MET cc_start: 0.9078 (tpp) cc_final: 0.8751 (mmm) REVERT: E 335 THR cc_start: 0.8659 (t) cc_final: 0.7935 (t) REVERT: F 167 LYS cc_start: 0.9210 (mppt) cc_final: 0.8888 (mtmt) REVERT: F 256 MET cc_start: 0.8650 (mmm) cc_final: 0.8139 (mmm) REVERT: d 250 MET cc_start: 0.5374 (mmt) cc_final: 0.4561 (mtm) REVERT: e 109 LYS cc_start: 0.9461 (ttpp) cc_final: 0.8990 (tppt) REVERT: g 66 LEU cc_start: 0.8452 (mt) cc_final: 0.7795 (tt) REVERT: g 133 PHE cc_start: 0.8610 (t80) cc_final: 0.8210 (t80) REVERT: g 295 LEU cc_start: 0.9010 (mt) cc_final: 0.8784 (mt) REVERT: g 323 MET cc_start: 0.9343 (mmp) cc_final: 0.8912 (mmm) REVERT: g 346 GLN cc_start: 0.8378 (mm-40) cc_final: 0.7946 (mt0) outliers start: 1 outliers final: 0 residues processed: 281 average time/residue: 0.1743 time to fit residues: 81.1834 Evaluate side-chains 213 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 41 optimal weight: 9.9990 chunk 79 optimal weight: 0.6980 chunk 230 optimal weight: 9.9990 chunk 299 optimal weight: 5.9990 chunk 184 optimal weight: 0.4980 chunk 194 optimal weight: 8.9990 chunk 352 optimal weight: 1.9990 chunk 142 optimal weight: 6.9990 chunk 319 optimal weight: 0.8980 chunk 280 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 GLN ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 HIS B 164 GLN B 269 GLN C 34 GLN C 164 GLN C 267 GLN C 334 ASN ** C 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN ** E 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 479 ASN ** d 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.051304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.042453 restraints weight = 189556.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.043782 restraints weight = 116961.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.044739 restraints weight = 80572.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.045460 restraints weight = 59567.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.045963 restraints weight = 46859.565| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27884 Z= 0.124 Angle : 0.659 11.934 37788 Z= 0.334 Chirality : 0.045 0.213 4447 Planarity : 0.005 0.099 4912 Dihedral : 6.534 92.717 3899 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.48 % Favored : 92.44 % Rotamer: Outliers : 0.10 % Allowed : 0.78 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.14), residues: 3558 helix: 0.57 (0.14), residues: 1453 sheet: -1.49 (0.24), residues: 477 loop : -1.95 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 418 TYR 0.017 0.001 TYR E 298 PHE 0.018 0.001 PHE E 271 TRP 0.005 0.001 TRP e 57 HIS 0.009 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (27883) covalent geometry : angle 0.65845 / 0.33 (37786) SS BOND : bond 0.00466 / 0.25 ( 1) SS BOND : angle 1.99415 / 1.33 ( 2) hydrogen bonds : bond 0.03728 / 2.58 ( 1236) hydrogen bonds : angle 4.73925 / 3.32 ( 3687) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 278 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.9078 (tp) cc_final: 0.8793 (tp) REVERT: A 157 MET cc_start: 0.8801 (ptp) cc_final: 0.7912 (mmt) REVERT: A 219 MET cc_start: 0.9108 (mmm) cc_final: 0.8830 (mmm) REVERT: A 251 MET cc_start: 0.8165 (ptp) cc_final: 0.7952 (ppp) REVERT: A 274 MET cc_start: 0.8452 (ptp) cc_final: 0.7930 (mtp) REVERT: A 314 MET cc_start: 0.8367 (mmm) cc_final: 0.7725 (mmm) REVERT: A 376 MET cc_start: 0.8894 (ptt) cc_final: 0.8360 (ppp) REVERT: A 498 MET cc_start: 0.8742 (mtm) cc_final: 0.8227 (mtp) REVERT: B 1 MET cc_start: 0.5670 (mmt) cc_final: 0.5386 (mmt) REVERT: B 236 GLN cc_start: 0.9306 (mt0) cc_final: 0.9084 (mt0) REVERT: B 251 MET cc_start: 0.7292 (tpt) cc_final: 0.6509 (tpt) REVERT: B 314 MET cc_start: 0.8182 (tpt) cc_final: 0.7696 (tpt) REVERT: B 355 ARG cc_start: 0.8943 (mmp-170) cc_final: 0.8490 (mmm160) REVERT: C 77 MET cc_start: 0.8254 (mtp) cc_final: 0.7997 (mtp) REVERT: C 234 THR cc_start: 0.9175 (p) cc_final: 0.8864 (p) REVERT: C 235 LEU cc_start: 0.9411 (mt) cc_final: 0.9183 (mt) REVERT: C 251 MET cc_start: 0.8694 (ttt) cc_final: 0.8443 (ttt) REVERT: C 295 HIS cc_start: 0.8904 (m-70) cc_final: 0.8628 (m-70) REVERT: D 170 LEU cc_start: 0.9285 (pt) cc_final: 0.8873 (mt) REVERT: D 183 MET cc_start: 0.8725 (mmp) cc_final: 0.8470 (mmm) REVERT: D 247 MET cc_start: 0.8560 (ttt) cc_final: 0.8229 (tpp) REVERT: E 79 MET cc_start: 0.9048 (mmt) cc_final: 0.8771 (mmp) REVERT: E 89 MET cc_start: 0.7994 (tpt) cc_final: 0.7662 (tpt) REVERT: E 247 MET cc_start: 0.8767 (tpt) cc_final: 0.8355 (tpp) REVERT: E 273 ASP cc_start: 0.8656 (t0) cc_final: 0.8430 (t70) REVERT: E 306 MET cc_start: 0.9057 (tpp) cc_final: 0.8757 (mmm) REVERT: E 335 THR cc_start: 0.8657 (t) cc_final: 0.7950 (t) REVERT: F 167 LYS cc_start: 0.9190 (mppt) cc_final: 0.8889 (mtmt) REVERT: F 256 MET cc_start: 0.8730 (mmm) cc_final: 0.8182 (mmm) REVERT: d 250 MET cc_start: 0.5350 (mmt) cc_final: 0.4500 (mtm) REVERT: e 24 LEU cc_start: 0.8706 (pt) cc_final: 0.8492 (pt) REVERT: e 109 LYS cc_start: 0.9393 (ttpp) cc_final: 0.8990 (tppt) REVERT: g 66 LEU cc_start: 0.7988 (mt) cc_final: 0.7639 (tt) REVERT: g 133 PHE cc_start: 0.8534 (t80) cc_final: 0.8147 (t80) REVERT: g 272 LYS cc_start: 0.8505 (tptt) cc_final: 0.7696 (tppt) REVERT: g 295 LEU cc_start: 0.9055 (mt) cc_final: 0.8708 (mt) REVERT: g 323 MET cc_start: 0.9318 (mmp) cc_final: 0.8995 (mmm) REVERT: g 346 GLN cc_start: 0.8388 (mm-40) cc_final: 0.7947 (mt0) outliers start: 3 outliers final: 0 residues processed: 281 average time/residue: 0.1715 time to fit residues: 80.1805 Evaluate side-chains 221 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 49 optimal weight: 4.9990 chunk 70 optimal weight: 0.2980 chunk 309 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 171 optimal weight: 10.0000 chunk 234 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 275 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 HIS B 164 GLN C 34 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN ** E 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.051145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.042313 restraints weight = 188875.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.043623 restraints weight = 116966.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.044589 restraints weight = 80504.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.045289 restraints weight = 59888.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.045773 restraints weight = 47213.872| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27884 Z= 0.130 Angle : 0.657 11.737 37788 Z= 0.334 Chirality : 0.045 0.212 4447 Planarity : 0.005 0.113 4912 Dihedral : 6.492 92.540 3899 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.39 % Favored : 92.52 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.14), residues: 3558 helix: 0.57 (0.14), residues: 1468 sheet: -1.50 (0.24), residues: 467 loop : -1.94 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 277 TYR 0.036 0.001 TYR C 330 PHE 0.017 0.001 PHE E 271 TRP 0.004 0.001 TRP e 57 HIS 0.009 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (27883) covalent geometry : angle 0.65681 / 0.33 (37786) SS BOND : bond 0.00451 / 0.24 ( 1) SS BOND : angle 2.08939 / 1.39 ( 2) hydrogen bonds : bond 0.03727 / 2.59 ( 1236) hydrogen bonds : angle 4.75330 / 3.33 ( 3687) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.9071 (tp) cc_final: 0.8789 (tp) REVERT: A 157 MET cc_start: 0.8810 (ptp) cc_final: 0.7916 (mmt) REVERT: A 274 MET cc_start: 0.8482 (ptp) cc_final: 0.8019 (mtp) REVERT: A 314 MET cc_start: 0.8402 (mmm) cc_final: 0.7755 (mmm) REVERT: A 376 MET cc_start: 0.8932 (ptt) cc_final: 0.8428 (ppp) REVERT: A 498 MET cc_start: 0.8727 (mtm) cc_final: 0.8176 (mtp) REVERT: B 1 MET cc_start: 0.5755 (mmt) cc_final: 0.5517 (mmt) REVERT: B 236 GLN cc_start: 0.9343 (mt0) cc_final: 0.9058 (mt0) REVERT: B 251 MET cc_start: 0.7257 (tpt) cc_final: 0.6215 (tpt) REVERT: B 314 MET cc_start: 0.8205 (tpt) cc_final: 0.7679 (tpt) REVERT: B 355 ARG cc_start: 0.9007 (mmp-170) cc_final: 0.8530 (mmm160) REVERT: C 77 MET cc_start: 0.8255 (mtp) cc_final: 0.8000 (mtp) REVERT: C 235 LEU cc_start: 0.9430 (mt) cc_final: 0.9227 (mt) REVERT: C 251 MET cc_start: 0.8727 (ttt) cc_final: 0.8452 (ttt) REVERT: C 295 HIS cc_start: 0.8965 (m-70) cc_final: 0.8679 (m-70) REVERT: D 170 LEU cc_start: 0.9275 (pt) cc_final: 0.8872 (mt) REVERT: D 183 MET cc_start: 0.8776 (mmp) cc_final: 0.8551 (mmm) REVERT: D 247 MET cc_start: 0.8617 (ttt) cc_final: 0.8190 (tpp) REVERT: D 374 MET cc_start: 0.8681 (mmm) cc_final: 0.8143 (mmt) REVERT: E 89 MET cc_start: 0.8014 (tpt) cc_final: 0.7646 (tpt) REVERT: E 162 TYR cc_start: 0.7288 (m-80) cc_final: 0.6974 (m-10) REVERT: E 247 MET cc_start: 0.8812 (tpt) cc_final: 0.8376 (tpp) REVERT: E 269 LEU cc_start: 0.9292 (tp) cc_final: 0.8879 (tt) REVERT: E 273 ASP cc_start: 0.8664 (t0) cc_final: 0.8433 (t0) REVERT: E 306 MET cc_start: 0.9094 (tpp) cc_final: 0.8793 (mmm) REVERT: E 335 THR cc_start: 0.8615 (t) cc_final: 0.7840 (t) REVERT: F 167 LYS cc_start: 0.9157 (mppt) cc_final: 0.8788 (mtmt) REVERT: F 256 MET cc_start: 0.8776 (mmm) cc_final: 0.8243 (mmm) REVERT: d 250 MET cc_start: 0.5332 (mmt) cc_final: 0.4488 (mtm) REVERT: e 109 LYS cc_start: 0.9429 (ttpp) cc_final: 0.8951 (tppt) REVERT: g 66 LEU cc_start: 0.8436 (mt) cc_final: 0.7788 (tt) REVERT: g 133 PHE cc_start: 0.8487 (t80) cc_final: 0.8109 (t80) REVERT: g 272 LYS cc_start: 0.8494 (tptt) cc_final: 0.7604 (tppt) REVERT: g 295 LEU cc_start: 0.9027 (mt) cc_final: 0.8803 (mt) REVERT: g 346 GLN cc_start: 0.8370 (mm-40) cc_final: 0.7954 (mt0) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.1710 time to fit residues: 78.5553 Evaluate side-chains 212 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 287 optimal weight: 0.5980 chunk 293 optimal weight: 4.9990 chunk 222 optimal weight: 8.9990 chunk 26 optimal weight: 0.8980 chunk 341 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 257 optimal weight: 0.9980 chunk 38 optimal weight: 8.9990 chunk 3 optimal weight: 0.6980 chunk 206 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 GLN ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 HIS B 164 GLN B 269 GLN C 34 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN ** E 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.051460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.042455 restraints weight = 190584.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.043783 restraints weight = 117360.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.044767 restraints weight = 80813.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.045445 restraints weight = 60186.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.045939 restraints weight = 47848.293| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27884 Z= 0.126 Angle : 0.664 12.028 37788 Z= 0.335 Chirality : 0.045 0.204 4447 Planarity : 0.005 0.097 4912 Dihedral : 6.447 91.073 3899 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.00 % Favored : 92.92 % Rotamer: Outliers : 0.03 % Allowed : 0.41 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.14), residues: 3558 helix: 0.61 (0.14), residues: 1469 sheet: -1.46 (0.24), residues: 469 loop : -1.90 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 277 TYR 0.033 0.001 TYR C 330 PHE 0.020 0.001 PHE D 111 TRP 0.005 0.001 TRP e 57 HIS 0.008 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (27883) covalent geometry : angle 0.66343 / 0.34 (37786) SS BOND : bond 0.00435 / 0.23 ( 1) SS BOND : angle 2.01531 / 1.34 ( 2) hydrogen bonds : bond 0.03729 / 2.60 ( 1236) hydrogen bonds : angle 4.68263 / 3.28 ( 3687) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3920.89 seconds wall clock time: 69 minutes 27.39 seconds (4167.39 seconds total)